Perfect! Exactly the information I needed.
Thanks,
Morgan
On Wed, Aug 10, 2011 at 4:15 PM, David Bapst dwba...@uchicago.edu wrote:
Morgan-
The node labels from ace() are the ID numbers used in the edge matrix
(you can see that with tree$edge, where 'tree' is your phylogeny
object), and the
Somewhere I wrote a function that samples at a series of
user-set timepoints and counts the # of lineages crossing
each timepoint -- this is pretty flexible, allows for
increases/decreases in diversity etc., let me know if the
other options aren't working for you I can dig it up...
On
Hi Rob.
Thanks for identifying the bug. This should be fixed, I hope, in the
newest version of phytools (v0.0-6; available:
http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/).
The way this function works is by first computing the heights above the
root of all the nodes (including tip
Hi Liam, Emmanuel, Nick, et al
Thanks for all the help.
Liam, I can confirm that your new function works fine on all the trees I've
tested (about 20). Thanks!
Some of my trees are pretty large (a few thousand taxa), so for interest's
sake I coded up Emmanuel's suggestion too.
The code is below
Hi Morgan all,
Some colleagues and I have been wondering something similar. We've tried
two approaches, and we would be grateful for any comments comparing them.
Like Morgan (I think), we do not have any predictor variables, just a
single trait whose value we would like to estimate for a tip
Hi everyone,
When performing Blomberg et al.'s test for phylogenetic signals, do the data
and/or branch lengths have to conform to the assumptions of Brownian motion as
discussed in Garland et al. (1992) and elsewhere, i.e. do contrasts have to be
adequately standardised? Or can data and
Hi all,
I'll make a new version of ltt.plot() that treats ultrametric and
non-ultrametric trees. After all, I don't see a logical reason why both
kinds of trees would be treated differently here. I'll add an option
backward (FALSE by default) so the time scale can start from the root,
and
